[gmx-users] Umbrella Sampling with 2 reaction coordinates

Dear gromacs users, I've performed umbrella sampling using 2 reaction coordinates (of the same geometry and dimensions and which I previously used for pulling in two phase spaces). Now I am trying to recover the PMF. Does g_wham support this scheme? Is it correct to obtain a 1D PMF by supplying

Re: [gmx-users] Umbrella sampling of peptide-membrane system

Dear John, Thank you very much for your advice. Best regards, Mijiddorj Hi, > > Justin's tutorial is not a fully generalized procedure for umbrella > sampling; it shows a workflow for one specific example which is not always > applicable to other systems. > > In general, you don't have to use

Re: [gmx-users] Umbrella sampling of peptide-membrane system

Hi, Justin's tutorial is not a fully generalized procedure for umbrella sampling; it shows a workflow for one specific example which is not always applicable to other systems. In general, you don't have to use position restraints for anything in umbrella sampling. Justin uses them to keep the

[gmx-users] Umbrella sampling of peptide-membrane system

Dear GMX users, I would like to ask about position restraint during the umbrella sampling. 1. Is it need to make position restraint of lipid bilayer during the umbrella sampling simulation? 2. The position restraint was used for the B chain of amyloid-beta peptides in prof. Justin's tutorial. Can

Re: [gmx-users] Umbrella sampling with restraint on the center of mass of ligand

On 1/15/20 6:32 AM, gmx user1 wrote: Dear GMX users I am doing umbrella sampling to obtain a PMF relative to the translocation of a ligand within a membrane protein. I want to add an harmonic potential to restrain the center of mass of the ligand in each window , similarly to the protocols

[gmx-users] Umbrella sampling with restraint on the center of mass of ligand

Dear GMX users I am doing umbrella sampling to obtain a PMF relative to the translocation of a ligand within a membrane protein. I want to add an harmonic potential to restrain the center of mass of the ligand in each window , similarly to the protocols used by Subramanian et al (

Re: [gmx-users] Umbrella Sampling on Lipid Bilayers, Pulling Issue and Umbrella Sampling Window Simulation Issues.

On 11/1/19 2:09 PM, Alexander Phillips wrote: Hello Everyone, I am currently running a CG MARTINI simulation on a bilayer of POPC Lipid in Water. I also have a single vitamin E in the mixture aswell (inside of the POPC bilayer). I am trying to perform umbrella sampling by pulling the vitamin

[gmx-users] Umbrella Sampling on Lipid Bilayers, Pulling Issue and Umbrella Sampling Window Simulation Issues.

Hello Everyone, I am currently running a CG MARTINI simulation on a bilayer of POPC Lipid in Water. I also have a single vitamin E in the mixture aswell (inside of the POPC bilayer). I am trying to perform umbrella sampling by pulling the vitamin E and measuring it's binding energy to POPC. I am

Re: [gmx-users] Umbrella sampling on lipid bilayer

> Dear gromacs users, > > Sorry for repeating my question. > > I didn't receive any email so I couldn't reply and I missed > > them. Hi, Justin replied in this mail: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-September/126735.html Best, John > > I am using following

[gmx-users] Umbrella sampling on lipid bilayer

Dear gromacs users, Sorry for repeating my question. I didn't receive any email so I couldn't reply and I missed them. I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. Ligand passes through the membrane,but along simulation, the size of

Re: [gmx-users] Umbrella sampling on lipid bilayer

On 9/25/19 5:50 AM, Mahsa Rezaei wrote: Dear Dr. Warren Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD ,

Re: [gmx-users] Umbrella sampling on lipid bilayer

Dear Dr. Warren Unfortunately,I missed your reply! Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD ,

[gmx-users] Umbrella sampling on lipid bilayer

Dear Dr. Warren Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD , temperature and pressure is good , so I

Re: [gmx-users] Umbrella sampling on lipid bilayer

Does it do that without using the pull code, i.e. just performing NPT simulation? What is physically happening? Sounds like the bilayer is unstable. What forcefield is this? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash

[gmx-users] Umbrella sampling on lipid bilayer

Dear gromacs users, I am using following pull code in md simulation for pulling a ligand across the plasma membrane model. Ligand passes through the membrane,but along simulation, the size of axis z increases. My size box is 8.52807 8.52807 14.0. And the pull distance is less than one-half

Re: [gmx-users] Umbrella sampling PMF using pull-geometry=direction

I am sorry I forgot to give the link in the last mail. https://indianinstituteofscience-my.sharepoint.com/:f:/g/personal/pradyumn_iisc_ac_in/EkAdkzcZsepHvbE1UDJPS5UBg2mENMYsRC2S0Z2DDWS9xQ?e=3GeICo On Fri, May 17, 2019 at 5:03 PM Pradyumn Sharma < cherpradyumnsha...@gmail.com> wrote: > Dear all

[gmx-users] Umbrella sampling PMF using pull-geometry=direction

Dear all I am trying to get a PMF for a small molecule translocation through an asymmetric membrane. I am doing it using pull-geometry= direction to do umbrella sampling at each window. I am getting a profile in which PMF of molecule in the bulk water at one side of the membrane is different from

[gmx-users] Umbrella sampling, choice of number of windows

Dear Gromacs Users, I would like to perform umbrella sampling on a protein using RMSD as CV. RMSD would be measured between the simulated structure and a so called active conformation and between an inactive conformation. To do that I am using PLUMED. However, I am new with US simulation and I

Re: [gmx-users] Umbrella Sampling - Changing force constant values between samples

On 10/22/18 1:45 PM, Dan Gil wrote: Hello, I am wondering if it is valid to use different force constant (k) values between samples for umbrella sampling. It seems that gmx_wham accepts different k values in a set, but I wanted to make sure this is OK. Should I be wary of any artifacts with

[gmx-users] Umbrella Sampling - Changing force constant values between samples

Hello, I am wondering if it is valid to use different force constant (k) values between samples for umbrella sampling. It seems that gmx_wham accepts different k values in a set, but I wanted to make sure this is OK. Should I be wary of any artifacts with these simulations? Best Regards, Dan

[gmx-users] Umbrella sampling histograms.

Hi, I did umbrella sampling for different distances of amino acid above surface. I found i special distance (1-1.2 nm above surface)histograms does not overlap. I did the sampling several times even for each 0.001 nm( of the distane between 1-1.2 nm) but the histo.xvg file didn't show ANY

[gmx-users] Umbrella Sampling: At diff force constant

Dear All: I am doing umbrella sampling for a dimer (Consist of two molecules stacking together, no physical bond). I tried different force constants, I got different PMF for each of them. Could you suggest me, How reliably can I choose force constant. Followings are the settings: ; Pull code

Re: [gmx-users] umbrella sampling tutorial

On 7/6/18 10:42 AM, hosein geraili wrote: Dear all, I have a question regarding the umbrella sampling tutorial. I am using the bash script to create the summary_distances.dat, but the problem is at first I would get the error "Unknown command-line option -o", then I used -oh instead of -o

[gmx-users] umbrella sampling tutorial

Dear all, I have a question regarding the umbrella sampling tutorial. I am using the bash script to create the summary_distances.dat, but the problem is at first I would get the error "Unknown command-line option -o", then I used -oh instead of -o which worked, but the problem is the 

Re: [gmx-users] Umbrella Sampling - Pulling distance larger 0.49 times box size Error during NPT equilibration

On 7/4/18 6:51 AM, Chenlin Lu wrote: Dear gromacs users, Hello, I am doing umbrella sampling to calculate the PMF puling an Au ion out of a protein channel. Basically, I followed the procedure given by Justin's tutorial. The configuration generation was finished correctly and the .mdp file

[gmx-users] Umbrella Sampling - Pulling distance larger 0.49 times box size Error during NPT equilibration

Dear gromacs users, Hello, I am doing umbrella sampling to calculate the PMF puling an Au ion out of a protein channel. Basically, I followed the procedure given by Justin's tutorial. The configuration generation was finished correctly and the .mdp file summary_distance.txt are shown below:

[gmx-users] Umbrella sampling

Hi, I do umbrella sampling for different distances of AA along surface and i calculated error by bootstrapping method. Error is less than 0.5 kj.mol-1 in 0.8to1.7 nm far from surface, but in 0.6to0.8 nm error is about 2 kj.mol-1 . The minimum energy is about -5kj.mol-1 at 0.65 nm. All windows

[gmx-users] Umbrella Sampling with water molecules flying away from the reference point

Dear GROMACS users, Currently I am experiencing a problem. At the moment I am trying to do a umbrella sampling with water going through a porous material. I have generate the configuration based on CV direction (1,1,1). However when I watch the movie back for individual simulation. I see the

Re: [gmx-users] Umbrella sampling: window distance - harmonic force constant

Okay. Thanks Justin! On 27.03.2018 21:12, Justin Lemkul wrote: On 3/27/18 4:44 AM, Hermann, Johannes wrote: Dear All, dear Justin, I am playing around with my umbrella sampling setup and I was looking at your paper which you linked in your umbrella sampling tutorial ("Assessing the

Re: [gmx-users] Umbrella sampling: window distance - harmonic force constant

On 3/27/18 4:44 AM, Hermann, Johannes wrote: Dear All, dear Justin, I am playing around with my umbrella sampling setup and I was looking at your paper which you linked in your umbrella sampling tutorial ("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular

[gmx-users] Umbrella sampling: window distance - harmonic force constant

Dear All, dear Justin, I am playing around with my umbrella sampling setup and I was looking at your paper which you linked in your umbrella sampling tutorial ("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics"). Up to a distance of 2nm you use a 0.1nm

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

Check the size of pullf-umbrellaX files(in a directory which gmx WHAM use them). MAYBE you refer for example a wrong pullf-umbrella0 file unintentionally. It happened to me. Check the size, they should be almost close to each other. Sent from my iPhone > On Mar 14, 2018, at 18:14, Ben Tam

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

n Thank you very much, Ben From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Awasthi, Neha <neha.awas...@biologie.uni-goettingen.de> Sent: Wednesday, March 14, 2018 15:16 To: gmx

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

s.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Awasthi, Neha <neha.awas...@biologie.uni-goettingen.de> Sent: Wednesday, March 14, 2018 15:16 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella Sampling - good histogram b

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Wednesday, March 14, 2018 3:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no re

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

Hi, That would generally suggest something divided by zero, or similar, eg because no data was in a histogram bin, etc. That behavior is a bug that we could perhaps fix if you would be so kind as to report it at https://redmine.gromacs.org. But the core problem remains that something about how

[gmx-users] Umbrella Sampling - good histogram but no result in profile

Dear all, I have a rather strange problem. Currently I am trying to get a PMF of a water molecule through a hydrophobic materials. At the end of using "gmx wham", I get a rather good histogram and it cover the whole range of the system. However at the making profile.xvg. I get the answer "nan"

Re: [gmx-users] Umbrella sampling

On 3/3/18 9:27 AM, rose rahmani wrote: Sorry, i can't understand, what do you mean"-zprof0" option? Could you please give me an example? Please read the gmx wham help information for a description. -Justin On 3 Mar 2018 16:47, "Justin Lemkul" wrote: On 3/3/18 7:02 AM,

Re: [gmx-users] Umbrella sampling

Sorry, i can't understand, what do you mean"-zprof0" option? Could you please give me an example? On 3 Mar 2018 16:47, "Justin Lemkul" wrote: On 3/3/18 7:02 AM, rose rahmani wrote: > Hi > > I use umbrella sampling to calculate PMF, for studying the interaction of > different

Re: [gmx-users] Umbrella sampling

On 3/3/18 7:02 AM, rose rahmani wrote: Hi I use umbrella sampling to calculate PMF, for studying the interaction of different aminoacids with nanosheet separately. But at the minimum distance from sheet, potential is zero for all PMF diagrams. I mean there isn't any positive potential even at

[gmx-users] Umbrella sampling

Hi I use umbrella sampling to calculate PMF, for studying the interaction of different aminoacids with nanosheet separately. But at the minimum distance from sheet, potential is zero for all PMF diagrams. I mean there isn't any positive potential even at closest distance of aminoacid from sheet.

[gmx-users] Umbrella sampling

Thank you so much for your detailed and useful answer,like always Honestly, this is part of my dissertation and i refer to this article mostly, which is too same.https://www.ncbi.nlm.nih.gov/pubmed/24606380 (I had to send this Message separately because Of size limitations) Sent from my iPhone

Re: [gmx-users] umbrella sampling

Oooh, i mean roomMate :))) Would you please answer my questions? Sent from my iPhone > On Feb 5, 2018, at 0:48, Rose wrote: > > > Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversations, > but i have some problems in my gmail which i can't open my

Re: [gmx-users] umbrella sampling

Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversations, but i have some problems in my gmail which i can't open my emails every times(i don't why but it's sth related to country ip&...) because Of that i have to use my roomate account,soy again Sent from my iPhone >

Re: [gmx-users] umbrella sampling

I don't know whether you're intentionally changing your email address or display name, but please refrain from doing so as it is very confusing who I'm talking to. On 2/4/18 4:00 PM, Nick Johans wrote: maybe this is irrelative but i expeienced in pulling that when i decrease dt from 2fs to

Re: [gmx-users] umbrella sampling

maybe this is irrelative but i expeienced in pulling that when i decrease dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were crushed before(when dt=2fs) so i had had to decrease nsteps or decrease pull_rate ,

Re: [gmx-users] umbrella sampling

On 2/4/18 3:25 PM, Rose wrote: Jeah,i meant grompp :))) and last question, i set constraint = h-Bonds, and dt=0.002 because Of that(since usually h-Bonds have Max frequency and if i assume them constraint so it's not reasonable to set dt=0.001 ) , is this assumption true? You can

Re: [gmx-users] umbrella sampling

Jeah,i meant grompp :))) and last question, i set constraint = h-Bonds, and dt=0.002 because Of that(since usually h-Bonds have Max frequency and if i assume them constraint so it's not reasonable to set dt=0.001 ) , is this assumption true? Sent from my iPhone > On Feb 4, 2018, at 23:30,

Re: [gmx-users] umbrella sampling

On 2/4/18 1:56 PM, Rose wrote: Thank you so much, Is it difference between using gmx tpbconv -extend 5ps OR use .gro file of last simulation as an input For new 5nS simulation?(continiuation=yes in .mdp file) The only reason to invoke grompp is if you're changing something about the

Re: [gmx-users] umbrella sampling

Thank you so much, Is it difference between using gmx tpbconv -extend 5ps OR use .gro file of last simulation as an input For new 5nS simulation?(continiuation=yes in .mdp file) Sent from my iPhone > On Feb 4, 2018, at 17:00, Justin Lemkul wrote: > > > >> On 2/2/18 10:44

Re: [gmx-users] umbrella sampling

On 2/2/18 10:44 AM, Rose wrote: Sent from my iPhone On Feb 2, 2018, at 19:01, Justin Lemkul wrote: On 2/2/18 8:43 AM, rose rahmani wrote: Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS simulation for each window. g_energy -f umbrella0.edr -o

Re: [gmx-users] umbrella sampling

and i have AA between sheet and wall.and it should get closer to sheet during pulling. How should i set the initial place of amino acid? it should have the minimum interaction with wall and sheet , am i right? On Fri, Feb 2, 2018 at 7:14 PM, Rose wrote: > > > Sent from my

Re: [gmx-users] umbrella sampling

Sent from my iPhone > On Feb 2, 2018, at 19:01, Justin Lemkul wrote: > > > >> On 2/2/18 8:43 AM, rose rahmani wrote: >> Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS >> simulation for each window. >> g_energy -f umbrella0.edr -o out.xvg >> 1

Re: [gmx-users] umbrella sampling

On 2/2/18 8:43 AM, rose rahmani wrote: Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS simulation for each window. g_energy -f umbrella0.edr -o out.xvg 1 Bond 2 Angle3 Proper-Dih. 4 Improper-Dih. 5 LJ-146 Coulomb-14

[gmx-users] umbrella sampling

Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS simulation for each window. >> g_energy -f umbrella0.edr -o out.xvg 1 Bond 2 Angle3 Proper-Dih. 4 Improper-Dih. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 9

Re: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

.ku...@ucdconnect.ie> Date: 28/1/18 12:53 am (GMT+10:00) To: gmx-us...@gromacs.org Subject: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error Hi, I'm doing umbrella sampling and running into the above error. I can't really increase the box size as that woul

[gmx-users] Umbrella sampling - Pull distance is larger than 0.49 times box size error

Hi, I'm doing umbrella sampling and running into the above error. I can't really increase the box size as that would make the system too big nor can I use pull-geometry = direction-periodic as I need to use NPT. But I'm confused on why I get this error in the first place because my periodic box

Re: [gmx-users] Umbrella Sampling

On 1/18/18 12:37 AM, Moradzadeh, Alireza wrote: Hi! I am trying to do umbrella sampling between two 2D-sheets. I did it according bevan lab tutorial the problem I encounter is that after pulling steps. I perform umbrella sampling with rate of 0.0 however, two sheets get back together and

[gmx-users] Umbrella Sampling

Hi! I am trying to do umbrella sampling between two 2D-sheets. I did it according bevan lab tutorial the problem I encounter is that after pulling steps. I perform umbrella sampling with rate of 0.0 however, two sheets get back together and initial configuration and final configuration are

[gmx-users] Umbrella Sampling/SMD pulling distance

Hi, I'm trying to do an SMD simulation to generate configurations for Umbrella sampling. I want to pull two groups together. I'm having trouble understanding why the pulled distance must smaller than the half the *shortest* box-vector length. I know that distance is calculated taking

Re: [gmx-users] Umbrella sampling-gmx distance

Oops,Sorrry. Sometimes big challenges make ones think hard and ignore obvious issues. Thank you so much Mr.justin and joao On Sat, Jan 13, 2018 at 4:01 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > The output is very explicitly telling you what the problem is. You didn't > provide

Re: [gmx-users] Umbrella sampling-gmx distance

The output is very explicitly telling you what the problem is. You didn't provide a topology. Pass one the the -s flag. How do you want the COM to be computed when you're not providing any masses? J On Jan 13, 2018 9:19 AM, "rose rahmani" wrote: > I'm relly sorry for

Re: [gmx-users] Umbrella sampling-gmx distance

I'm relly sorry for asking you again and again but... GROMACS: gmx distance, VERSION 5.1.4 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com of group 6'

Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

On 1/12/18 7:09 AM, rose rahmani wrote: I had this problem but i couldn't solve it. But i can tell you just a temporary solution; Don't use -sep with trjconv,then use the output conf as an input for gmx distance. it probably gives you sth like this; time distances

Re: [gmx-users] Umbrella sampling-gmx distance

On 1/11/18 11:38 AM, rose rahmani wrote: [ ZnS ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45..

Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

I had this problem but i couldn't solve it. But i can tell you just a temporary solution; Don't use -sep with trjconv,then use the output conf as an input for gmx distance. it probably gives you sth like this; time distances 0.0001.75372870.02386010.0428935

[gmx-users] umbrella sampling Protein_ligand complex distance calculation

Hi Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very fine. so I following the same tutorial for ligand-protein complex. I have pulled the ligand over 300ps using following MD_pull.mdp and also generated series of cordinate files (conf0.gro-conf300.gro) but problem is

[gmx-users] Umbrella sampling-gmx distance

[ ZnS ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45.. [ Protein ] 761 762 763 764 765 766 767

Re: [gmx-users] Umbrella Sampling-gmx distance

On 1/11/18 9:50 AM, rose rahmani wrote: still like this You're not using the command syntax shown in the link I provided. -Justin # This file was created Thu Jan 11 09:46:46 2018 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable:

Re: [gmx-users] Umbrella Sampling-gmx distance

still like this # This file was created Thu Jan 11 09:46:46 2018 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # Command line: # gmx distance -n index.ndx -f conf0.gro -oxyz dist0.xvg

Re: [gmx-users] Umbrella Sampling-gmx distance

On 1/11/18 3:43 AM, rose rahmani wrote: Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp file for pulling: integrator = md dt = 0.001 nsteps

[gmx-users] Umbrella Sampling-gmx distance

Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp file for pulling: integrator = md dt = 0.001 nsteps = 250 nstxout = 5000

Re: [gmx-users] umbrella sampling, LINCS WARNING

On 1/4/18 2:48 AM, rose rahmani wrote: Hello; I'm doing umbrella sampling, protein is getting closer to ZnS, but i get some step files and run crashed just 107sec to end. Would it be because of protein got very close to ZnS? Would you please help me? A COM distance of 0.3 nm is going to

[gmx-users] umbrella sampling, LINCS WARNING

Hello; I'm doing umbrella sampling, protein is getting closer to ZnS, but i get some step files and run crashed just 107sec to end. Would it be because of protein got very close to ZnS? Would you please help me? With regards - this is pullf.xvg 0. -0.000579208 0.0020

Re: [gmx-users] Umbrella sampling

-users@maillist.sys.kth.se Subject: Re: [gmx-users] Umbrella sampling - Message from Mark Abraham <mark.j.abra...@gmail.com> - Date: Fri, 22 Dec 2017 00:42:31 + From: Mark Abraham <mark.j.abra...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-use

Re: [gmx-users] Umbrella sampling

- Message from Mark Abraham <mark.j.abra...@gmail.com> -     Date: Fri, 22 Dec 2017 00:42:31 +     From: Mark Abraham <mark.j.abra...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gromacs.org       Cc: gro

Re: [gmx-users] Umbrella sampling

- Message from "Jefferies D.F." <dfj1...@soton.ac.uk> -     Date: Tue, 19 Dec 2017 20:56:34 +     From: "Jefferies D.F." <dfj1...@soton.ac.uk> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gr

Re: [gmx-users] Umbrella sampling

boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of > sp...@iacs.res.in [sp...@iacs.res.in] > Sent: Tuesday, December 19, 2017 6:21 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Umbrella sampling > &g

Re: [gmx-users] Umbrella sampling

[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of sp...@iacs.res.in [sp...@iacs.res.in] Sent: Tuesday, December 19, 2017 6:21 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Umbrella sampling - Message from Dhaniram Mahato <bioinfo...@gmail.

Re: [gmx-users] Umbrella sampling

- Message from Dhaniram Mahato <bioinfo...@gmail.com> -     Date: Tue, 19 Dec 2017 21:30:05 +0800     From: Dhaniram Mahato <bioinfo...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gromacs.org Hi, There cou

Re: [gmx-users] Umbrella sampling

- Message from Dhaniram Mahato <bioinfo...@gmail.com> -     Date: Tue, 19 Dec 2017 21:30:05 +0800     From: Dhaniram Mahato <bioinfo...@gmail.com> Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling       To: gmx-us...@gromacs.org Hi, There cou

Re: [gmx-users] Umbrella sampling

Hi, There could be format problem. You can create your own .dat files by typing it. You have probably copied it from somewhere. I hope it will work then. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html Thanks -- Gromacs Users mailing list * Please search

[gmx-users] Umbrella sampling

Hi all I am doing umbrella sampling taking distance between COM as a reaction coordinate. when I am trying to calculate PMF using the following command  gmx wham -it tpr-files.dat -if pullf-files.dat  -o free.xvg -hist hist.xvg I got an error  Program:     gmx wham, version 2016.3 Source file:

Re: [gmx-users] Umbrella sampling

On Sat, Dec 16, 2017 at 12:38 PM, rose rahmani wrote: > and also i want protein get closer to ZnS sheet during pulling in just Z >> direction and straightforward to sheet( like one straight line to sheet), >> is this suitable md_pull.mdp file for this approach? > > is it

Re: [gmx-users] Umbrella sampling

and also i want protein get closer to ZnS sheet during pulling in just Z direction and straightforward to sheet( like one straight line to sheet), is this suitable md_pull.mdp file for this approach? and what about time?is 4nS suitable for each window? Thanks indeed On Sat, Dec 16, 2017 at 10:05

Re: [gmx-users] Umbrella sampling

Hi, I try to use umbrella sampling for calculating PMF. i change distance between protein and ZNS nanosheet. I use gomacsV4.5.4 after minimization and equilibration. i use: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr this is md_pull.mdp: integrator =

[gmx-users] umbrella sampling

Hello, I'm beginner in GROMACS. I'm trying to do umbrella sampling, but profile.xvg file has nan value! i don't really know why this happens? This is md_umbrella.mdp. ; Pull code pull= umbrella pull_ngroups= 1 pull_group0 = MX pull_group1

Re: [gmx-users] Umbrella sampling simulation stopped in middle.

On 12/4/17 1:33 AM, Sailesh Bataju wrote: Hi, I've started to pull a dimer of isobutane molecules as a production md after npt equilibriation. Here is the md_pull.mdp file for production md. ; Umbrella pulling, production md ; preprocessing parameters title = Umbrella Sampling ; run

[gmx-users] Umbrella sampling simulation stopped in middle.

Hi, I've started to pull a dimer of isobutane molecules as a production md after npt equilibriation. Here is the md_pull.mdp file for production md. ; Umbrella pulling, production md ; preprocessing parameters title = Umbrella Sampling ; run parameters integrator = md ; leap-frog integrator for

Re: [gmx-users] Umbrella sampling

On 12/3/17 8:01 AM, rose rahmani wrote: On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul wrote: On 11/28/17 12:23 AM, rose rahmani wrote: Hello; I took 2000 configuration from trajconv. Amino acid is in its normal shape till almost conf1000.gro(and a little more). But in

Re: [gmx-users] Umbrella sampling

On 12/3/17 8:42 AM, rose rahmani wrote: I need to share you sth which just happened; i run md_pull.mdp in two steps: 1--1nS( dt= 0.001 nsteps=100) , 2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS( dt= 0.001 nsteps=200) and scond time for 4nS (dt=0.001

Re: [gmx-users] Umbrella sampling

I need to share you sth which just happened; i run md_pull.mdp in two steps: 1--1nS( dt= 0.001 nsteps=100) , 2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS( dt= 0.001 nsteps=200) and scond time for 4nS (dt=0.001 nsteps=400) and The protein was in normal

Re: [gmx-users] Umbrella sampling

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul wrote: > > > On 11/28/17 12:23 AM, rose rahmani wrote: > >> Hello; >> >> I took 2000 configuration from trajconv. Amino acid is in its normal shape >> till almost conf1000.gro(and a little more). But in for example >> conf1300.gro

Re: [gmx-users] umbrella sampling

On 11/29/17 2:45 PM, rose rahmani wrote: Hello; would you please send me Mr.lemkul's article link ? i can't find them. It's linked here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html If you need something regarding my published research,

[gmx-users] umbrella sampling

Hello; would you please send me Mr.lemkul's article link ? i can't find them. Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

Re: [gmx-users] umbrella sampling

On Mon, Nov 27, 2017 at 2:30 AM, rose rahmani wrote: > > > On Mon, Nov 27, 2017 at 1:55 AM, Alex wrote: > >> Hi, >> >> The answer is clearly in the error, just read it please: >> 2.848793 > 0.49 * (4/2) where 4 is the box length. >> >>> But i

Re: [gmx-users] Umbrella sampling

On 11/28/17 10:00 AM, rose rahmani wrote: Would "pull_geometry=periodic-distance" be another solution for it? No. That affects how the reaction coordinate distance is calculated, not the PBC treatment, which is intrinsic to any simulation using PBC. -Justin On Tue, Nov 28, 2017 at 5:11

Re: [gmx-users] Umbrella sampling

Would "pull_geometry=periodic-distance" be another solution for it? On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul wrote: > > > On 11/28/17 12:23 AM, rose rahmani wrote: > >> Hello; >> >> I took 2000 configuration from trajconv. Amino acid is in its normal shape >> till almost

Re: [gmx-users] Umbrella sampling

On 11/28/17 12:23 AM, rose rahmani wrote: Hello; I took 2000 configuration from trajconv. Amino acid is in its normal shape till almost conf1000.gro(and a little more). But in for example conf1300.gro amino acid was disintegrated. What does it mean? Would you please help me? Bonds can't

Re: [gmx-users] Umbrella sampling

Hello; I took 2000 configuration from trajconv. Amino acid is in its normal shape till almost conf1000.gro(and a little more). But in for example conf1300.gro amino acid was disintegrated. What does it mean? Would you please help me? Best regards Rose On Sun, Nov 26, 2017 at 12:39 AM, Justin

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